@Article{CiCP-19-3,
author = {},
title = {Simulating Biofilm Deformation and Detachment with the Immersed Boundary Method},
journal = {Communications in Computational Physics},
year = {2016},
volume = {19},
number = {3},
pages = {682--732},
abstract = {<p style="text-align: justify;">We apply the immersed boundary (or IB) method to simulate deformation
and detachment of a periodic array of wall-bounded biofilm colonies in response to a
linear shear flow. The biofilm material is represented as a network of Hookean springs
that are placed along the edges of a triangulation of the biofilm region. The interfacial
shear stress, lift and drag forces acting on the biofilm colony are computed by
using fluid stress jump method developed by Williams, Fauci and Gaver [Disc. Contin.
Dyn. Sys. B 11(2):519–540, 2009], with a modified version of their exclusion filter.
Our detachment criterion is based on the novel concept of an averaged equivalent
continuum stress tensor defined at each IB point in the biofilm which is then used to
determine a corresponding von Mises yield stress; wherever this yield stress exceeds a
given critical threshold the connections to that node are severed, thereby signalling the
onset of a detachment event. In order to capture the deformation and detachment behaviour
of a biofilm colony at different stages of growth, we consider a family of four
biofilm shapes with varying aspect ratio. For each aspect ratio, we varied the spacing
between colonies to investigate role of spatial clustering in offering protection against
detachment. Our numerical simulations focus on the behaviour of weak biofilms (with
relatively low yield stress threshold) and investigate features of the fluid-structure interaction
such as locations of maximum shear and increased drag. The most important
conclusions of this work are: (a) reducing the spacing between colonies reduces
drag by from 50 to 100% and alters the interfacial shear stress profile, suggesting that
even weak biofilms may be able to grow into tall structures because of the protection
they gain from spatial proximity with other colonies; (b) the commonly employed detachment
strategy in biofilm models based only on interfacial shear stress can lead to
incorrect or inaccurate results when applied to the study of shear induced detachment
of weak biofilms. Our detachment strategy based on equivalent continuum stresses
provides a unified and consistent IB framework that handles both sloughing and erosion modes of biofilm detachment, and is consistent with strategies employed in many
other continuum based biofilm models.</p>},
issn = {1991-7120},
doi = {https://doi.org/10.4208/cicp.161214.021015a},
url = {https://global-sci.com/article/80271/simulating-biofilm-deformation-and-detachment-with-the-immersed-boundary-method}
}